High-throughput capture of cis-rearrangement and trans-rearrangement sequence [LAM-HTGTS]

Cell cycle is a major determinant of DNA double-strand break (DSB) repair pathway choice with homologous recombination (HR) that is most active in S phase cells and non-homologous end-joining (NHEJ) that dominates in G1 phase cells. A third less well-defined mechanism, 'alternative end-joining', has been shown to promote error-prone repair in NHEJ- or HR-deficient cells. Here, we have used a physiologic system of NHEJ-mediated genomic rearrangements induced by the site-specific RAG1/2 endonuclease in G1 cells to investigate the fate of unrepaired G1 DSBs upon entry into the cell cycle. We show that, in the absence of XRCC4, alternative end-joining rescues RAG-induced DSB repair and promotes chromosome translocations upon G1 cell cycle exit. Overall design: We performed linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) on mouse v-Abl/Bcl2 immortalized pro-B cell lines which included genotypes WT, Xrcc4-/-, p53-/- and Xrcc4-/- p53-/-. Igk-J4 primer was used as bait to capture cis-rearrangement sequence within Igk loci and trans-rearrangement sequence with whole genome-wide. The captured of cis- and trans-rearrangement sequences with Igk-J4 were analyzed and compared among cycling cells, v-Abl kinase inhibitor treated and released cells. *Please note that each wig processed data was generated from all replicates together and is linked to the corresponding rep1 sample records.